Problem in "index" function in recognizing repeating substrings

[monkfan]

Most revered monks,
The built-in index function seems to be able to recognize only the first substring given two identical substrings from a string. My code below:

#!/usr/bin/perl -w
use strict;

my $str = 'NNNNNATCGNNNNATCG';
my @substr  = qw(ATCG ATCG);
foreach (@substr)
{
   my $id = index($str,$_);
   print "$id\n"; 
}

Returns:

5
5

How can I overcome this problem such that the index function can recognize the second substrings in the correct position? Returning this instead:

5
13

[reasonablekeith]

#!/usr/bin/perl -w
use strict;

my $str = 'NNNNNATCGNNNNATCG';
my @substr  = qw(ATCG ATCG);
my $id = -1;
foreach (@substr)
{
   $id = index($str, $_, $id+1);
   print "$id\n"; 
}

[Tanalis]

index accepts a position to start from as a third argument. If you track $id to figure out where in the string you are, you should be able to avoid matching the first instance repeatedly.

See the docs for more information.

[ysth]

Do you want:

my $str = "ATCGATCGAT";
my @substr = qw(ATCG CGAT);

to give 0 and 2 or 0 and 6?

If the latter, do

$id = -1;
foreach (@substr)
{
   my $id = index($str,$_,$id);
   print "$id\n";
   $id += length($_);
}

[reasonablekeith]

I've pointed this out to him before, didn't get a response then either.

[monkfan]

Dear ysth,
Thanks a lot for pointing out the important case that I missed.
With your example above, I will opt for the 'closest' substrings namely:

0 and 2

If the latter

You mean the 'former'? Because, having tested your above code, I think it already gave that answer..
Please correct me if I'm wrong.

[saberworks]

No, his code clearly gives 0 and 6. If you want 0 and 2, try this:

#!/usr/bin/perl
use strict;

my $str = 'ATCGATCGAT';
my @sub = qw(ATCG CGAT);

my $id = 0;

foreach (@sub) {
    $id = index($str, $_, $id);
    print "$id\n";
    $id++;
}